As the tyre size gets bigger so naturally its circumference will increase, I’ve just had this problem on rebuild where I had to drop the trye size to fit between the chain stays.
Without a photo I’m trying to understand what exactly you mean maybe I’m missing something :-
You say the distance to the seat post do you mean the seat post half way down to the BB when looking at the wheel at 9.0’ clock ? or are you referring to the seat post bridge where the brake caliper is ?.
Either way it seems a very small distance,
I’m asking a stupid question – is the rear wheel fully back in the drop out slots ?